Smothering fecal-oral coronavirus spread

Besides respiratory symptoms, diarrhea is one of the other commonly observed disease manifestations in patients with COVID-19. Zang et al. used organoid cultures of epithelial lining cells from human small and large intestine as an in vitro model system to study SARS-CoV-2 entry and replication in enterocytes. Mature enterocytes expressing the highest levels of the angiotensin-converting enzyme 2 (ACE2) viral receptor were susceptible to productive infection. Two related membrane-bound serine proteases, TMPRSS2 and TMPRSS4, enhanced virus entry into enterocytes. While a subset of patients with COVID-19 shed high levels of viral RNA in feces, experiments examining the effect of simulated human colonic fluid on the virus suggest that shed virus is rapidly inactivated during transit through the colon, strongly suppressing the potential for further spread of the infection through a fecal-oral route.

Abstract

Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA are frequently observed in COVID-19. However, it is unclear whether SARS-CoV-2 replicates in the human intestine and contributes to possible fecal-oral transmission. Here, we report productive infection of SARS-CoV-2 in ACE2+ mature enterocytes in human small intestinal enteroids. Expression of two mucosa-specific serine proteases, TMPRSS2 and TMPRSS4, facilitated SARS-CoV-2 spike fusogenic activity and promoted virus entry into host cells. We also demonstrate that viruses released into the intestinal lumen were inactivated by simulated human colonic fluid, and infectious virus was not recovered from the stool specimens of patients with COVID-19. Our results highlight the intestine as a potential site of SARS-CoV-2 replication, which may contribute to local and systemic illness and overall disease progression.

INTRODUCTION

Coronavirus disease 2019 (COVID-19) has emerged as a new world pandemic, infecting millions and causing substantial morbidity and mortality. This outbreak is caused by a novel severe acute respiratory syndrome coronavirus, SARS-CoV-2 (1, 2), which belongs to the family of Coronaviridae, a group of enveloped, nonsegmented, positive-sense RNA viruses. Currently, there are no clinically approved countermeasures available for COVID-19. Severe SARS-CoV-2–associated disease occurs more frequently in the elderly and those with specific comorbidities (e.g., diabetes and obesity), although the basis for this remains largely unknown. SARS-CoV-2 also has a more protracted disease time course and prolonged viral RNA shedding compared with some other respiratory viruses, raising questions about other potential modes of transmission.

The attachment of SARS-CoV-2 to the target cell is initiated by interactions between the spike glycoprotein (S) and its cognate receptor, angiotensin-converting enzyme 2 (ACE2) (2–5). Following receptor engagement, SARS-CoV-2 S is processed by a plasma membrane–associated type II transmembrane serine protease, TMPRSS2, before membrane fusion, which is essential to release the viral contents into the host cell cytosol (3, 6). Both ACE2 and TMPRSS2 are expressed highly in the gastrointestinal (GI) tract, in particular by intestinal epithelial cells (IECs), the predominant target cells for many human enteric viruses. Several animal CoVs are natural enteric pathogens, cause GI diseases, and spread by the fecal-oral route (7). Notable GI symptoms including abdominal pain and diarrhea have been observed in 20 to 50% of patients with COVID-19 and sometimes precede the development of respiratory illness (8–10). In a U.S. cohort–based study, 61% of patients exhibited GI symptoms (11). Substantial amounts of SARS-CoV-2 RNA are detected in stool specimens from patients with COVID-19 (12–16). Infectious virus was not isolated from the feces of patients with COVID-19 in a recent systematic study (17), although two studies report virus isolation (18, 19). The fecal shedding data raise the possibility that SARS-CoV-2 could potentially be transmitted via the fecal-oral route (20).

In the present study, we aimed to address the following questions: (i) Does SARS-CoV-2 infect human IECs? (ii) If so, what host factors mediate efficient replication? (iii) Are there infectious viruses shed in the fecal samples of patients with COVID-19? Here, we present evidence that SARS-CoV-2 infects human mature enterocytes from the apical surface and triggers epithelial cell fusion. TMPRSS2 and TMPRSS4 serine proteases mediate this process by inducing cleavage of the S protein and enhancing membrane fusion. We also found that simulated human colonic fluid rapidly inactivates SARS-CoV-2 in vitro, rendering viral RNA noninfectious in the stool specimens. Our findings have mechanistic and translational relevance and enhance our understanding of COVID-19 pathogenesis.

RESULTS

SARS-CoV-2 infects human intestinal enteroids

In the intestine, ACE2 functions as a chaperone for the sodium-dependent neutral amino acid transporter B0AT1 (encoded by SLC6A19) on IECs and regulates microbial homeostasis (21, 22). ACE2 expression is substantially higher in the small intestine than in all the other organs, including the lung, in both humans and mice (fig. S1, A and B). Given these data, we assessed whether SARS-CoV-2 can infect IECs as a first step for understanding its implications for fecal-oral transmission. We performed single-cell RNA sequencing (scRNA-seq) to capture the global transcriptomics in all IEC subsets in the mouse small intestinal epithelium (Fig. 1A, left). ACE2 mRNA was predominantly seen in Cd26+Epcam+Cd44−Cd45− mature enterocytes (Fig. 1A, right) (23, 24). In addition, bulk RNA-seq revealed that primary human ileum enteroids had substantially higher mRNA levels of all known CoV receptors, including ACE2, than the colonic epithelial cell line HT-29 and other non-IEC human cell lines (fig. S1C). Quantitative polymerase chain reaction (qPCR) confirmed abundant ACE2 transcript levels in both human duodenum- and ileum-derived enteroids (fig. S1D). ACE2 protein colocalized with actin at the apical plasma membrane of human enteroid monolayers (Fig. 1B). Higher ACE2 levels correlated with the maturity of enterocytes present in differentiated enteroids (Fig. 1B), consistent with our scRNA-seq findings (Fig. 1A). In three-dimensional (3D) Matrigel embedded enteroids, ACE2 had an almost perfect colocalization with villin (fig. S1E), an IEC marker that localizes most strongly to the brush border of the intestinal epithelium.

SARS-CoV-2 actively replicates in ACE2+ human mature enterocytes

To further characterize the potential SARS-CoV-2 route of infection, we used the 2D monolayer system (27), with a clear polarity and separation of apical and basal sides that represent the luminal and lamina propria compartments, respectively. Human IECs were preferentially (>1000-fold) infected by VSV-SARS-CoV-2 from the apical surface compared with the basolateral side (Fig. 2A). These data are consistent with apical ACE2 expression (Fig. 1B and fig. S1E). The newly produced virus progeny was released predominantly from the apical side into the lumen (Fig. 2B), suggesting a possibility of viral shedding and accumulation in feces in patients with COVID-19.

(A) Human duodenum enteroids in monolayer, cultured in either maintenance (MAINT) or differentiation (DIFF) conditions, were apically or basolaterally infected with 1.5 × 105 PFU of VSV-SARS-CoV-2 for 24 hours. The expression of VSV-N was measured by RT-qPCR and normalized to that of GAPDH. (B) Supernatants in both apical and basal chambers were collected from (A) and were subjected to a TCID50 assay to measure the amount of infectious virus. (C) Differentiated duodenum enteroids in monolayer were apically infected with 2.5 × 105 PFU of infectious SARS-CoV-2 virus (MOI = 0.5) for 8 hours. The expression of SARS-CoV-2 N was measured by RT-qPCR using a TaqMan assay and normalized to that of GAPDH. (D) Differentiated ileum enteroids in monolayer were apically or basolaterally infected with 2.5 × 105 PFU of infectious SARS-CoV-2 virus (MOI = 0.5) for 8 hours. The expression of SARS-CoV-2 N was measured by RT-qPCR using a TaqMan assay and normalized to that of GAPDH. (E) Same as (C) except that enteroids were fixed and stained for SARS-CoV-2 S (green), ACE2 (red), and nucleus (DAPI, blue). Scale bars, 32 μm. SARS-CoV-2–infected ACE2-positive cells are enlarged in the inset (yellow box). (F) SARS-CoV-2–infected duodenum monolayers were imaged along the Z stacks and sectioned for YZ planes (top) and reconstructed for 3D images (bottom). For all figures except (C) to (E), experiments were repeated at least three times with similar results. (C) to (E) were performed twice with technical duplicates in each experiment. Data are represented as mean ± SEM. Statistical significance is indicated (*P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001).

To define the specific IEC subset(s) targeted by SARS-CoV-2, we infected duodenal enteroids with VSV-SARS-CoV-2 and costained with different IEC markers. GFP signal was found principally in CD26+ mature villous absorptive enterocytes (fig. S2A). To a lesser extent, the VSV-SARS-CoV-2 virus also replicated in undifferentiated enteroids (Figs. 1, C and E, and 2A), suggesting that transit-amplifying cells or intestinal stem cells support some level of infection. Using a clinical isolate of the wild-type infectious SARS-CoV-2 virus, we confirmed that viral RNA increased by 320-fold within the first 8 hours of infection (Fig. 2C). Mirroring the VSV-SARS-CoV-2 virus, wild-type SARS-CoV-2 infection also occurred preferentially (>10,000-fold) at the apical surface of the intestinal epithelium compared with the basolateral side (Fig. 2D). In addition, SARS-CoV-2 infection of enteroid monolayers suggested that ACE2+ mature enterocytes were the predominant target cells in the gut epithelium (Fig. 2E). Staining of S protein revealed interesting punctate-like structures within the infected IECs (Fig. 2E). A 3D reconstruction of confocal images showed that the S protein was concentrated toward the apical surface (Fig. 2F), suggesting a potential mechanism of polarized viral assembly and subsequent apical release. Compared with rotavirus, a prototypic enteric pathogen that is known to trigger interferon (IFN) signaling (23), wild-type SARS-CoV-2 infection induced a comparably robust type I IFN (IFN-β) and type III IFN (IFN-λ) expression in human IECs from both apical and basolateral infections (fig. S2B).

Similar to wild-type SARS-CoV-2 that induces syncytia formation (28), VSV-SARS-CoV-2 infection was associated with cell-cell fusion (fig. S2C) causing syncytia formation between primary IECs in both 2D monolayer (fig. S2D) and 3D Matrigel (fig. S2E and movie S1). The cell fusion may lead to subsequent cytopathic effect and a breach of the intestinal epithelium integrity and thus may have implications regarding the common GI symptoms seen in patients with COVID-19 (29–33).

TMPRSS2 and TMPRSS4, but not ST14, promote SARS-CoV-2 entry

Recent studies suggest that the membrane-bound TMPRSS2 protease cleaves the S protein and promotes SARS-CoV-2 entry (3, 6, 34). Two other serine proteases in the same family, TMPRSS4 and matriptase (encoded by ST14), were highly expressed in human IECs (Fig. 3A). Previous studies indicated that both TMPRSS4 and ST14 facilitate influenza A virus infection but neither had a role in SARS-CoV infection (35–38). In our mouse scRNA-seq dataset, TMPRSS4 and ST14 were expressed in ACE2+ mature enterocytes, while TMPRSS2 was primarily expressed in ACE2− secretory IECs (fig. S3A).

(A) Bulk RNA-seq results of intestine-specific serine protease expression in HEK293, Huh7.5, H1-Hela, and HT-29 cells and human ileum enteroids. (B) HEK293 cells were transfected with pcDNA3.1-V5-ACE2, DDP4, or ANPEP for 24 hours (left), or transfected with indicated plasmid combination for 24 hours (right), and infected with 1.5 × 105 PFU of VSV-SARS-CoV-2 for 24 hours. The expression of VSV-N was measured by RT-qPCR and normalized to that of GAPDH. (C) HEK293 cells stably expressing human ACE2 were transfected with SARS-CoV-2 S and TMPRSS2 or TMPRSS4 for 48 hours. Cells were treated with trypsin at 0.5 μg/ml for 10 min. The levels of S and GAPDH were measured by Western blot. The intensity of bands was quantified by ImageJ and shown as percentage of the bottom band versus the top band in each lane. (D) HEK293 cells stably expressing human ACE2 were transfected with TMPRSS2 or TMPRSS4 for 24 hours, incubated with 5.8 × 105 PFU of VSV-SARS-CoV-2 on ice for 1 hour, washed with cold phosphate-buffered saline for three times, and shifted to 37°C for another hour. The expression of VSV-N was measured by RT-qPCR and normalized to that of GAPDH. (E) Wild-type (WT) or human ACE2-expressing HEK293 cells were transfected with SARS-CoV-2 S and GFP, with or without TMPRSS2 or TMPRSS4 for 24 hours. The red arrows highlight the formation of large syncytia. Scale bars, 100 μm. For all figures except (A), experiments were repeated at least three times with similar results. RNA-seq in (A) was performed once with duplicate samples. Data are represented as mean ± SEM. Statistical significance is indicated (*P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001).

To dissect the entry pathway of SARS-CoV-2 in IECs, we set up an ectopic expression system in human embryonic kidney (HEK) 293 cells to evaluate VSV-SARS-CoV-2 infection. As reported (2, 5), ACE2 conferred permissiveness to VSV-SARS-CoV-2 infection (Fig. 3B and fig. S3B). Although TMPRSS2 alone did not mediate viral infection, coexpression of TMPRSS2 with ACE2 resulted in enhanced infectivity (Fig. 3B). Moreover, expression of TMPRSS4, but not ST14, also resulted in a significant increase in the levels of viral RNA and infectious virus in the presence of ACE2 (Fig. 3B and fig. S3C). Coexpression of TMPRSS4 and TMPRSS2 had an additive effect and enabled maximal infectivity in cell culture (Fig. 3B and fig. S3, C to E).

We hypothesized that TMPRSS4, like TMPRSS2, might function as a cell surface serine protease to enhance S cleavage and promote viral entry. To test this idea, we coexpressed full-length SARS-CoV-2 S protein in an HEK293 cell line that stably expresses ACE2 with or without additional introduction of TMPRSS2 or TMPRSS4. In mock-transfected cells, we readily observed the full-length S and a cleaved product that corresponded to the size of S1 fragment (Fig. 3C), presumably cleaved by furin protease that is ubiquitously expressed (39). Compared with the positive control exogenous trypsin treatment, expression of TMPRSS2 or TMPRSS4 promoted S cleavage, as evidenced by the reduction of full-length S and increased levels of S1 protein (Fig. 3C).

On the basis of these results, we hypothesized that TMPRSS serine proteases facilitate virus infection by inducing S cleavage and exposing the fusion peptide for efficient viral entry. TMPRSS4 expression did not affect virus binding at 4°C but led to an increase in infection as evidenced by enhanced viral gene transcription 1 hour after warming cells to 37°C (Fig. 3D). We next determined the influence of TMPRSS2 or TMPRSS4 on SARS-CoV-2 S protein–mediated cell-cell fusion. Previous work with SARS-CoV and MERS-CoV (Middle East respiratory syndrome coronavirus) suggests that S-mediated membrane fusion occurs in a cell type–dependent manner (40). Ectopic expression of S protein alone was sufficient to induce syncytia formation, independent of virus infection (Fig. 3E). This process was dependent on expression of both ACE2 and TMPRSS serine proteases. TMPRSS4 expression triggered S-mediated cell-cell fusion, although to a lesser extent than TMPRSS2 (Fig. 3E). These studies show that TMPRSS2 and TMPRSS4 activate SARS-CoV-2 S and enhance membrane fusion.

TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection in enteroids

To further probe the mechanism of action of TMPRSS serine proteases, we designed an in vitro coculture system where ACE2 and S were expressed on target and donor cells, respectively. On the basis of the scRNA-seq data (fig. S3A), we constructed an HEK293 cell line that coexpressed ACE2 and TMPRSS4 to mimic mature enterocytes and another HEK293 cell line that expressed TMPRSS2 to mimic goblet or other secretory IEC types (Fig. 4A, left). Target cells were transfected with GFP and mixed at 1:1 ratio with SARS-CoV-2 S–containing donor cells that were transfected with TdTomato. TMPRSS4 could function in cis, i.e., on the same cells as ACE2, and induced fusion of GFP-positive cells but not in trans (Fig. 4A, right). In comparison, TMPRSS2 could act both in cis and in trans and its expression on adjacent cells resulted in larger syncytia formation (Fig. 4A, right).

(A) Schematic diagram of SARS-CoV-2 infection of human mature enterocytes. SARS-CoV-2 particles, host proteins, and host cells are not proportional to the true sizes. On the basis of the scRNA-seq data (fig. S3A), TMPRSS4 is more highly expressed than TMPRSS2 on mature absorptive enterocytes and TMPRSS2 is more highly expressed on secretory cells than TMPRSS4. FPKM, fragments per kilobase per million mapped reads. (B) GFP-expressing HEK293 cells were mixed at 1:1 ratio and cocultured with HEK293 cells expressing SARS-CoV-2 S and TdTomato for 24 hours (right). Note the formation of cell-cell fusion (yellow), highlighted by black arrows. (C) Images in (B) were quantified based on the intensity of yellow signals. T2: TMPRSS2; T4: TMPRSS4. (D) Human duodenum enteroids in 3D Matrigel were transduced with lentiviruses encoding Cas9 and sgRNA against TMPRSS2 or TMPRSS4 (oligonucleotide information in table S1). Gene knockout (KO) enteroids were seeded into monolayers and infected with 1.5 × 105 PFU of VSV-SARS-CoV-2 for 24 hours. The expression of VSV-N was measured by RT-qPCR and normalized to that of GAPDH. (E) Human duodenum, ileum, and colon enteroids were infected with 2.9 × 105 PFU of VSV-SARS-CoV-2 for 24 hours. The levels of indicated viral and host transcripts were measured by RT-qPCR and normalized to that of GAPDH. (F) Human duodenum enteroids seeded into collagen-coated 96-well plates were differentiated for 3 days; pretreated with SBTI (50 μg/ml), 10 μM camostat mesylate, or 10 μM E-64d for 30 min; and infected with 1.5 × 105 PFU of VSV-SARS-CoV-2 for 24 hours. The expression of VSV-N was measured by RT-qPCR and normalized to that of GAPDH. All experiments were repeated at least three times with similar results. Data are represented as mean ± SEM. Statistical significance is indicated (*P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001).

To determine the function of TMPRSS serine proteases in facilitating SARS-CoV-2 S–mediated infection of primary human IECs, we used CRISPR-Cas9 gene editing to deplete TMPRSS2 or TMPRSS4 expression in human duodenum enteroids. Efficient knockout was confirmed by immunoblotting (fig. S4A). Abrogation of TMPRSS4 expression led to a fourfold reduction in VSV-SARS-CoV-2 replication in human enteroids greater than seen for TMPRSS2 knockout cells (Fig. 4B). We examined the ACE2, TMPRSS2, and TMPRSS4 mRNA levels in a panel of human duodenum, ileum, and colon intestinal enteroids from different donors and correlated the susceptibility to VSV-SARS-CoV-2 infection (Fig. 4C). Higher ACE2 levels correlated with infection, although TMPRSS2 and TMPRSS4 expression also showed a positive correlation as well (fig. S4B). ACE2, TMPRSS2, and TMPRSS4 mRNA levels were not altered by VSV-SARS-CoV-2 infection (fig. S4C).

In parallel, we also tested the effect of pharmacological inhibition of TMPRSS serine proteases on virus replication. We pretreated enteroids with camostat mesylate, a selective inhibitor of TMPRSS over other serine proteases, including trypsin, prostasin, and matriptase (41). Whereas camostat treatment significantly inhibited VSV-SARS-CoV-2 infection, soybean trypsin inhibitor (SBTI) and E-64d, a cysteine protease inhibitor that blocks cathepsin activity and inhibits SARS-CoV-2 infection in Vero cells (3), did not affect virus replication in enteroids (Fig. 4D). Together, our data support a model in which SARS-CoV-2, at least in TMPRSS+ human IECs, is more reliant on the membrane-bound serine proteases (Fig. 4A, left) than SARS-CoV and other CoVs and can efficiently use both TMPRSS2 and endosome-localized cathepsins as alternative routes of entry (42, 43).

SARS-CoV-2 is rapidly inactivated in the human GI tract

Our results suggest that SARS-CoV-2 viruses can infect human IECs apically and are released via the apical route into the lumen (Fig. 2). Human enteric viruses that spread via the fecal-oral route typically withstand the harsh environment in the GI tract, including the low pH of gastric fluids, bile, and digestive enzymes in the small intestine, dehydration, and exposure to multiple bacterial byproducts in the colon. We investigated the stability of a recombinant SARS-CoV-2 mNeonGreen reporter virus (44) in different simulated human gastric and intestinal fluids. Compared with rotavirus, which is transmitted by the fecal-oral route (45), SARS-CoV-2 lost infectivity in the low pH simulated gastric fluid at 10 min after incubation (fig. S5A). However, there was residual SARS-CoV-2 virus in simulated human small intestinal fluid that contains biological surfactants including taurocholic acid sodium salt and lecithin (Fig. 5A). In contrast, SARS-CoV-2 was inactivated by certain components in the simulated human colonic fluids (Fig. 5A). The virus titers decreased by fivefold within 1 hour, and little infectious virus was detectable at the 24-hour time point (Fig. 5A). In contrast, rotavirus remained stable in all simulated gastric and enteric fluids tested (fig. S5, A and B).

(A) SARS-CoV-2-mNeonGreen virus (2.5 × 105 PFU) was incubated with M199 medium, simulated human small intestinal (SI) fluid, or simulated human large intestinal (LI) fluid for indicated time points at 37°C. The virus was subsequently serially diluted and added to MA104 cells for 24 hours, and GFP signals were scanned by Typhoon 5. (B) Stool specimens from 10 patients with COVID-19 were collected and subjected to qPCR experiments to quantify the absolute levels of SARS-CoV-2 N gene. (A) was performed once in quadruplicate. (B) was performed once. Data are represented as mean ± SEM. Statistical significance is indicated (*P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001).

Combined with the human enteroid results (Figs. 1 and 2), we reasoned that the SARS-CoV-2 replicates in human IECs but may then be rapidly inactivated in the lumen of the colon. We collected stool specimens from a small group of patients with COVID-19. From 3 of 10 fecal samples, we detected high RNA copy numbers of SARS-CoV-2 viral genome (Fig. 5B). However, we were unable to recover any infectious virus using a highly sensitive cell-based assay (6) as compared with the medium spiked with cell culture–derived wild-type SARS-CoV-2 viruses (fig. S5C).

DISCUSSION

In this study, we addressed an important basic and clinically relevant question: Is the persistent viral RNA seen in the stool of patients with COVID-19 infectious and transmissible? We showed that despite SARS-CoV-2’s ability to establish robust infection and replication in human IECs (Figs. 1 and 2), the virus is rapidly inactivated by simulated human colonic fluid and a limited number of viral RNA–positive fecal samples did not contain infectious virus. Thus, the large quantities of viral RNA that transit through the GI tract and shed into the feces may not carry substantial infectious risk. Because of the limitation of our sample size, we cannot definitely conclude that fecal-oral transmission of COVID-19 does not occur. Another potential caveat is that the sample collection depends on the transit time. In other words, if patients with COVID-19 have rapid transit colonic motility because of either small bowel or colon pathophysiology or in the setting of diarrhea, the feces may still contain residual infectivity. However, our data are consistent with the previous reports from SARS-CoV and MERS-CoV publications, which concluded that, despite long duration of viral RNA shedding, no infectious virus could be recovered from the patients’ feces (46, 47).

Intriguingly, the simulated small intestinal fluid, which contains taurocholic acid sodium salt and lecithin, important surfactant components of the bile, did not inactivate virus as expected (Fig. 5A). Further experiments are being performed with bile acids and bile salts that act as detergents in gut. Recent studies showed a heavy glycosylation of SARS-CoV-2 S protein (48), and it is possible that the glycan coating confers some stability against the enzymatic digestion and bile salt solubilization. Two recent publications demonstrated that SARS-CoV-2 has unique stability in the laboratory environment (49, 50). Further work is needed to determine which bioactive component(s) of the simulated colonic fluid that is absent from small intestinal fluid may function to inactivate virus in vivo.

Recent work from multiple groups has shown a key role of TMPRSS2 in cleaving SARS-CoV-2 S protein. We provide data that besides TMPRSS2, TMPRSS4 also increases SARS-CoV-2 infectivity, at least in gut epithelial cells (Figs. 3 and 4). We observed an intriguing additive effect of the two enzymes, as both target single arginine or lysine residues. We speculate that this synergy stems from a distinct cellular and subcellular localization in neighboring cells (Fig. 4A). Future work with recombinant proteins and enzymatic digestion may help address whether S cleavage is sequential and whether the two enzymes act on different sites on the S protein.

Last, we observed syncytia formation in human enteroids. These results may have implications for virus cell-cell spread and evasion of antibody neutralization (51). During the revision of this work, two manuscripts were published that examined SARS-CoV-2 infection of human IECs (52, 53). Cell fusion was also observed, although it was not discussed. It is unclear at this point whether the fused IECs will still undergo anoikis or an alternative accelerated cell death, which may cause a breach in barrier integrity and give rise to some of the GI pathology and symptomatology seen in patients with COVID-19. It is possible that, in the small intestine, additional proteases such as trypsin enhance viral infection and pathogenesis by triggering more robust IEC fusion. Although viruses are not released into the basolateral compartment, a leaky gut might allow virus to disseminate to other systemic organs, including the lung and liver. This hypothesis, although speculative, is consistent with the clinical observation that, in some patients with COVID-19, the GI symptoms precede the respiratory illness (8, 9). Whether the gut serves as a primary site of infection and contributes to systemic diseases in individual patients requires further study.

MATERIALS AND METHODS

Study design

The goal of this study was to examine the possibility of SARS-CoV-2 replication in the human intestine and potential fecal-oral transmission. A number of approaches and techniques, including scRNA-seq, human intestinal organoids, VSV-SARS-CoV-2-S-GFP chimeric virus (25), and wild-type SARS-CoV-2 virus, were used. The numbers of experimental and technical replicates in each group and the statistical analysis applied are described in the figure legends and in the “Statistical analysis” section.

Plasmids, cells, reagents, and viruses

Plasmids

Human ACE2, DPP4, ANPEP, TMPRSS2, TMPRSS4, and ST14 were cloned into a pcDNA3.1/nV5-DEST vector with an N-terminal V5 tag and a neomycin selection marker. Human TMPRSS2 and TMPRSS4 were also cloned into a pLX304 lentiviral vector with a C-terminal V5 tag and a blasticidin selection marker. pEGFP-N1 and pCMV-TdTomato were commercially purchased from Clontech. Codon-optimized SARS-CoV-2 S was a gift from N. J. Krogan at the University of California, San Francisco (UCSF) (54).

Viruses

VSV-SARS-CoV-2 GFP reporter chimeric virus was constructed by P.W.R. and S.P.J.W using the SARS-CoV-2 Wuhan-Hu-1 spike and the VSV Indiana strain (25). The virus was propagated in MA104 cells in T175 flasks. SARS-CoV-2 strain 2019-nCoV/USA-WA1/2020 was obtained from N. Thornburg at the Centers for Disease Control and Prevention. A mNeonGreen SARS-CoV-2 reporter virus was used as previously reported (44). Virus was passaged once in Vero CCL81 cells (ATCC) and titrated by focus-forming assay in Vero-E6 cells. Plaque assays were performed in MA104 cells seeded in six-well plates using an adapted version of the rotavirus plaque assay protocol (23). Human rotavirus WI61 strain was propagated as described before (55). TCID50 (median tissue culture infectious dose and FFU (focus-forming unit) assays were performed in MA104 cells seeded in flat-bottom 96-well plates using serial dilutions. Virus infections were performed with the initial inoculum removed at 1 hour after adsorption.

Human intestinal enteroids

One duodenum (#CD94), five ileum (#14-75, #211D, #262D-2, #265D, and #251D-2), and one colon (#235A) enteroids were used in this study. All enteroids were derived from deidentified tissue from healthy subjects without inflammatory bowel disease who were undergoing colonoscopy and provided informed consent at Stanford University or Washington University School of Medicine. In brief, enteroids were cultured in maintenance medium (advanced DMEM/F12 medium supplemented with L-WRN–conditioned medium that contains Wnt-3a, R-spondin 3, and Noggin) in 3D Matrigel in 24-well plates (56). For passing enteroids, Rho-associated, coiled-coil containing protein kinase (ROCK) inhibitor Y-27632 and glycogen synthase kinase–3 (GSK-3) inhibitor CHIR99021 were added. For differentiation, conditioned medium was replaced with 50% Noggin in the form of recombinant proteins. Enteroids, when required, were digested into single cells using TrypLE (Thermo Fisher Scientific) and seeded into collagen-coated Transwells (0.33 cm2, 0.4-μm pore size, Polycarbonate, Thermo Fisher Scientific #07-200-147) in Y-27632–supplemented maintenance medium in 24-well plates. Transepithelial electrical resistance (TEER) measurement was performed using the Millicell ERS-2 Voltohmmeter (Millipore). Enteroids in monolayers were used for virus infection if the cultures had TEER greater than 1000 ohm·cm2 at 5 days after seeding. For CRISPR-Cas9 knockout, enteroids in 3D Matrigel were digested with 5 mM EDTA and transduced with lentiviral vectors encoding Cas9 and single-guide RNA (sgRNA) against TMPRSS2 or TMPRSS4 (see table S1) in the presence of polybrene (8 μg/ml). At 48 hours after transduction, puromycin (2 μg/ml) was added to the maintenance medium. Puromycin was adjusted to 1 μg/ml upon the death of untransduced control enteroids.

RNA extraction and qPCR

Total RNA was extracted from cells using RNeasy Mini kit (Qiagen), and reverse transcription (RT) was performed with High-Capacity RT kit and random hexamers as previously described (57). qPCR was performed using the AriaMx (Agilent) with a 25-μl reaction, composed of 50 ng of complementary DNA (cDNA), 12.5 μl of Power SYBR Green or TaqMan master mix (Applied Biosystems), and 200 nM both forward and reverse primers. All SYBR Green primers and TaqMan probes used in this study are listed in table S1.

scRNA-seq analysis

Five-day-old 129/Sv strain suckling mice were obtained from the Greenberg laboratory breeding colony at Stanford University. IECs were isolated from small intestine tissue pooled from two males and one female by EDTA-dithiothreitol extraction method, and cell sorting was performed as previously described (23, 59). Cells were stained with LIVE/DEAD Aqua Dead Cell Stain Kit (Thermo Fisher Scientific), and live cells were sorted using a BD FACSAria II flow cytometer. Preparation of single-cell suspensions was performed at the Stanford Genome Sequencing Service Center. Cell suspensions were processed for scRNA-seq using Chromium Single Cell 3′ Library and Gel Bead Kit v2 (10× Genomics, PN-120237) according to 10× Genomics guidelines. Libraries were sequenced on an Illumina NextSeq 500 using 150 cycles high output V2 kit (Read 1-26, Read 2-98, and Index 1-8 bases). The Cell Ranger package (v3.0.2) was used to align high-quality reads to the mouse genome (mm10). Normalized log expression values were calculated using the scran package (60). Highly variable genes were identified using the FindVariableGenes function (Seurat, v2.1) as described (61). Batch effects from technical replicates were removed using the MNN algorithm as implemented in the batchelor package’s (v1.0.1) fastMNN function. Imputed expression values were calculated using a customized implementation (https://github.com/kbrulois/magicBatch) of the MAGIC (Markov affinity-based graph imputation of cells) algorithm (62) and optimized parameters (t = 2, k = 9, ka = 3). Cells were classified as dividing or resting using a pooled expression value for cell cycle genes (Satija Lab Website: regev_lab_cell_cycle_genes). For UMAP and tSpace embeddings, cell cycle effects were removed by splitting the data into dividing and resting cells and using the fastMNN function to align the dividing cells with their resting counterparts. Dimensionality reduction was performed using the UMAP algorithm, and nearest neighbor alignments for trajectory inference and vascular modeling were calculated using the tSpace algorithm. Pooled expression of all viral genes was calculated using the AddModuleScore function from the Seurat package.

Human Institutional Review Board approval

COVID-19 patient–derived biospecimens (stool) were collected with an Institutional Review Board (IRB)-approved protocol with written informed consent (IRB #202003085) by the Washington University Human Research Protection Office and under the management of the Institute of Clinical and Translational Sciences. The collection and use of human tissue for establishing primary epithelial cell culture or organoid culture were approved by the Washington University Human Research Protection Office (IRB #201404112) and collected with written informed consent by the Washington University Digestive Diseases Research Core Center Biobank Core.

Statistical analysis

All bar graphs were displayed as means ± SEM. Statistical significance in data in Fig. 2C was calculated by Student’s t test using Prism 8.4.1 (GraphPad). Statistical significance in data in Figs. 1 (C and E), 2 (A and D), 3 (B and D), 4A, and 5A and figs. S2B and S3C was calculated by pairwise analysis of variance (ANOVA) using Prism 8. Simple linear regression was performed to calculate R2 and P values for fig. S4B. Statistical significance of all data is presented as asterisks (*P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001). All experiments other than Figs. 1A, 2 (C to E), and 5 (A and B) and fig. S5 (A and C) have been repeated at least three times. The scRNA-seq analysis (Fig. 1A and fig. S3A) was performed once using small intestinal tissue pooled from three mice. Bulk RNA-seq analysis (Fig. 3A and fig. S1C) was performed once for each cell type using two duplicate samples.

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Acknowledgments: We appreciate the assistance from M. Williams (Molecular Microbiology Media and Glassware Facility), W. Betty (Molecular Microbiology Imaging Facility), F. Zhao (Division of Rheumatology), and P. Mudd (Division of Emergency Medicine) for fecal specimen collection. SARS-CoV-2 TaqMan probe and viral RNA standards were prepared by A. Bailey (Division of Infectious Diseases). The scRNA-seq experiments were performed at the Genome Sequencing Service Center by Stanford Center for Genomics and Personalized Medicine Sequencing Center with the assistance from Y. Ryan and K. Hennig and financially supported by NIH grant S10OD020141. The schematic diagram in Fig. 4A was generated with the help from BioRender (biorender.com). The collection of fecal samples was supported by ICTS COVID-19 Research Funding Program with NIH grants UL1 TR002345, KL2 TR002346, and TL1 TR002344. Funding: This work is supported by NIH grants K99/R00 AI135031 and R01 AI150796 awarded to S.D., NIH grant R01 AI125249 and VA Merit grant GRH0022 awarded to H.B.G., NIH contracts and grants (75N93019C00062 and R01 AI127828) and the Defense Advanced Research Project Agency (HR001117S0019) to M.S.D., NIH grants NIDDK P30 DK052574 and R01 DK109384 and the Lawrence C. Pakula MD IBD Innovation Fund to M.A.C., NIH grant F32 AI138392 to B.T.M., and unrestricted funds from Washington University School of Medicine and R37 AI059371 to S.P.J.W. Author contributions: X.W., H.B.G., M.S.D., M.A.C., S.P.J.W., and S.D. conceived the study. R.Z., M.F.G.C., and S.D. conducted the majority of the experiments. B.T.M. carried out wild-type SARS-CoV-2 infection experiments. Q.Z. performed RNA extraction and TCID50 assays. P.W.R. constructed and rescued the VSV-SARS-CoV-2 virus, and Z.L. sequenced the S region. N.M.S. provided four human ileum and one colon enteroid samples. K.F.B. performed the scRNA-seq analysis. S.D. wrote and revised the original manuscript with contributions and input from all authors. Competing interests: H.B.G. currently consults for the following companies: Sanofi, Pfizer, FluGen, and Aridis. M.S.D. is a consultant for Inbios, Eli Lilly, Vir Biotechnology, NGM Biopharmaceuticals, and Emergent BioSolutions and on the Scientific Advisory Board of Moderna. The Diamond laboratory at Washington University School of Medicine has received sponsored research agreements from Moderna. An invention disclosure was filed with Washington University in St. Louis by P.W.R. and S.P.J.W. for the recombinant VSV-SARS-CoV-2 used herein. Data and materials availability: The scRNA-seq results of mouse small intestinal cells were deposited at Gene Expression Omnibus (GEO) of NCBI (GSE149907). The VSV-SARS-CoV-2 virus is available upon request from S.P.J.W. through a material transfer agreement with Washington University School of Medicine in St. Louis. All other data needed to evaluate the conclusions in the paper are present in the paper or the Supplementary Materials.